The fun bit about Kindles being registered at the factory is that if you've ever bought a Kindle book before (on an old Kindle or an app) your books get pre-loaded as well. I wish they hadn't released a 3G-less model though; it's a major convenience boost (no need to even think about a network unless you're in a very remote bit of the country)
But iTunes is required to update my ipod to iOS 5 :-)
I've never been able to get large pdf's onto my ipod without itunes. Can't email them because they're too big, and the ipod cannot browse local shared directories.
You can also add PDFs to iBooks on the device without iTunes -- not sure about epub files though.